Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2-NAPHTHYL-GUANINE ADDUCT IN ANTI ORIENTATION
DOI:10.2210/pdb2w8l/pdb   NDB ID: 2W8L
2W8L

Entry 2W8L supersedes 2V4T

Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 51549.90
    Molecule: DNA POLYMERASE IV
    Polymer: 1 Type: protein Length: 358
    Chains: A
    EC#: 2.7.7.7   
    Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS
    Organism: Sulfolobus solfataricus P2
    Gene Names: dbh dpo4 SSO2448
    UniProtKB: Protein Feature View | Search PDB | Q97W02  
    Molecule: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3'
    Polymer: 2 Type: dna Length: 14
    Chains: P
    Details: 14 BASE PRIMER DNA 5'-GGG GGA AGG ATT CC-3'
    Molecule: 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3'
    Polymer: 3 Type: dna Length: 18
    Chains: T
    Details: 18 BASE TEMPLATE DNA 5'-TCA C(NPG)G AAT CCT TCC CCC-3'
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Sulfolobus solfataricus   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1JX4   CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE 
    1JXL   CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE 
    1N48   Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION 
    1N56   Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION 
    1RYR   REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION 
    1RYS   REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION 
    1S0M   CRYSTAL STRUCTURE OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCTIN A TERNARY COMPLEX WITH A DNA POLYMERASE 
    1S0N   SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT 
    1S0O   SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT 
    1S10   SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT 
    1S97   DPO4 WITH GT MISMATCH 
    1S9F   DPO WITH AT MATCHED 
    2AGO   FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS 
    2AGP   FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS 
    2AGQ   FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS 
    2ASD   OXOG-MODIFIED INSERTION TERNARY COMPLEX 
    2ASJ   OXOG-MODIFIED PREINSERTION BINARY COMPLEX 
    2ASL   OXOG-MODIFIED POSTINSERTION BINARY COMPLEX 
    2ATL   UNMODIFIED INSERTION TERNARY COMPLEX 
    2AU0   UNMODIFIED PREINSERTION BINARY COMPLEX 
    2BQ3   DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE 
    2BQR   DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE 
    2BQU   DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE 
    2BR0   DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE 
    2C22   EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4 
    2C28   EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4 
    2C2D   EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4 
    2C2E   EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4 
    2C2R   EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4 
    2J6S   TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP. 
    2J6T   TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP. 
    2J6U   TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DGTP. 
    2JEF   THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOTIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING 
    2JEG   THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING 
    2JEI   THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING 
    2JEJ   THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING 
    2UVR   CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS 
    2UVU   CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS 
    2UVV   CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS 
    2UVW   CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS 
    2V4Q   POST-INSERTION COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH M1DG CONTAINING TEMPLATE DNA 
    2V4R   NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE 
    2V9W   COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND 
    2VA2   COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND 
    2VA3   COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND 
    2W8K   Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2-NAPHTHYL-GUANINE ADDUCT IN SYN ORIENTATION 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    DGT
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    DGT C10 H16 N5 O13 P3
    2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
    DGT:2W8L
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    DGT
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    DGT
    N/Ain BindingDB
    N/Ain BindingMoad
    Kd: 29000 nM - data from PDBbind  
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    DOC
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    DOC C9 H14 N3 O6 P DC dnaLinking
    N2G
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    N2G C21 H22 N5 O7 P nonPolymer
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:2W8L
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Eoff, R.L.,  Zhang, H.,  Egli, M.,  Guengerich, F.P.

    Deposition:   2009-01-16
    Release:   2009-01-27
    Last Modified (REVDAT):   2010-08-25

    Previous versions:  2V4T
     
  •   Revision History    Hide
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    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.00
    R-Value: 0.226 (obs.)
    R-Free: 0.282
    Space Group: P 21 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 95.92 α = 90.00 
    b = 103.83 β = 90.00 
    c = 52.49 γ = 90.00